Archive for May, 2010

My post last week about Creationism by region set off a fair number of follow up questions. I’ve actually probed the GSS evolution related variables a lot in the past, but I thought I would put it together in one post in a simple fashion for new readers. I used the SCITEST4 variable since its sample size is the largest. The question asked was: ” Human beings developed from earlier species of animals.” It was asked between 1993 and 2000.

There are four answers, definitely true, probably true, probably not true, definitely not true. I put the frequencies in a table below, but I thought it would be useful to have one number to summarize the propensity toward creationism in a demographic. Therefore, I created a simple “index of creationism.” The formula to create it is pretty obvious:

If the Index of Creationism for a demographic was zero, that means that everyone in the demographic accepted that evolution was definitely true. In contrast, if it was three, that means that everyone in the demographic believed that evolution was definitely not true. The bar chart below has the Indices of Creationism sorted. Below it is a table with the frequencies as well (unsorted, clustered by demographic kind).

A few preliminaries. First, if you have not updated to the new feed yet, please do do! Go into your RSS and check that your link is: http://feeds.feedburner.com/GeneExpressionBlog. If not, change it. Or if you’re too lazy to check, just follow the link and subscribe again and delete the old feed. Please.

Second, I will be traveling a fair amount over the next four weeks. I won’t post as regularly or frequently. I may not do a link round up, because whole days may pass before I get on the internet! I figured I should mention this because last fall when I didn’t post for four days (I was at the Singularity Summit) a few people made inquiries as to my health. Also, if you haven’t had a comment approved already (in which case your comment goes through automatically), there is a serious probability that you’ll be stuck in the mod queue for days for the next month. Apologies ahead, but please be chill about that.

Affluent Qataris Seek What Money Cannot Buy. This is a very amusing article. The fact is that Gulf Arabs, who have benefited from windfall wealth which they did not earn in any way, have a really minimal work ethic and maximal sense of entitlement. It’s bad form today to dismiss whole populations like this, but I don’t really care, it’s true, everyone who has worked in the Gulf knows this. The New York Times tries to maintain an air of neutral detachment, but the author of the linked article couldn’t keep it up. The piece is about the frustration that Qataris face due to discrimination in employment opportunities because employers stereotype them as relatively lazy, unqualified, and demanding (though it’s really hard to match semi-slave labor too! So “entitled” might mean “refusal to work 18 hours a day for 7 days a week” for minimal pay). Employers and coworkers treat them like the special education kid in the classroom. But that’s because that’s the rational thing to do. We all know, and can admit, that children who have large trust funds can often (though not always!) grow up to be spoiled and rendered far less productive than they would be otherwise because of wealth unearned. Same with Qataris. The final paragraph makes the journalists’ bemusement rather crystal clear:

“Moza al-Malki, a family therapist, said she was angry, too. She said that she had lost her teaching position when she complained that an Indian woman was hired to run a counseling center that she said she had set up. “We are all angry for staying at home,” she said.

A moment earlier, she turned to the Filipino woman walking one step behind her — a servant carrying bags — and told her to go look around the mall they were in while Ms. Malki ordered breakfast. Ms. Malki ordered a croissant with cheese, sent it back because it was too hard, and then settled on an omelet.”

You probably are aware that different populations have different tolerances for high altitudes. Himalayan sherpas aren’t useful just because they have skills derived from their culture, they’re actually rather well adapted to high altitudes because of their biology. Additionally, different groups seem to have adapted to higher altitudes independently, exhibiting convergent evolution. But in terms of physiological function they aren’t all created equal, at least in relation to the solutions which they’ve come to to make functioning at high altitudes bearable. In particular, it seems that the adaptations of the peoples of Tibet are superior than those of the peoples of the Andes. Superior in that the Andean solution is more brute force than the Tibetan one, producing greater side effects, such as lower birth weight in infants (and so higher mortality and lower fitness).

The Andean region today is dominated by indigenous people, and Spanish is not the lingua franca of the highlands as it is everyone in in the former colonial domains of Spain in the New World. This is largely a function of biology; as in the lowlands of South America the Andean peoples were decimated by disease upon first contact (plague was spreading across the Inca Empire when Pizzaro arrived with his soldiers). But unlike the lowland societies the Andeans had nature on their side: people of mixed or European ancestry are less well adapted to high altitudes and women without tolerance of the environment still have higher miscarriage rates.

Check out the #bg2010 hash-tag on twitter. There’s a lot of interesting tidbits. Here are some tweets from the presentation on the Neandertal genome in relation to the Denisova hominin (a.k.a. “X-woman”):

lukejostins SP: The Denisova finger is from the Neanderthal line, but didn’t interbreed with humans, hence looking like an outgroup
…
dgmacarthur: SP claims that Neanderthals and Denisova archaics are more closely related than either are to humans; intriguing.
…
dgmacarthur: SP: next steps: generate 10-20X coverage of Neanderthal, sequence other archaic humans (e.g. Denisova).

Science fiction dates as quickly as any genre, and Bradbury is not entirely immune to this. The futuristic rocket ships he wrote about in 1950 look a lot like the first-generation NASA rockets; the music of the future is Rachmaninoff and Duke Ellington; and in the terrifying “Mars is Heaven,” the planet bears an eerie resemblance to Green Bluff, Ill., right down to Victorian houses “covered with scrolls and rococo.” But the reason Bradbury’s stories still sing on the page is that, despite all his humanoid robots, automated houses, and rocket men, his interest is not in future technologies but in people as they live now—and how the proliferation of convenient technology alters the way we think and the way we treat each other.

Leamer on the State of Econometrics. This is a podcast, but very interesting. I’ve pulled back from getting too complicated in my data analysis with the GSS in large part because it started to become obvious how easy it was to secretly massage the model to get a statistically significant result. Instead I’ve leaned toward presenting simple descriptive frequencies and providing the variables so that readers can follow up themselves. In that way more complicated digging into the data can (theoretically) occur in the comments and so operate on a level of transparency. Otherwise I’d feel obligated to record and list all the various “quick & dirty” regressions and controls I ran, and that gets tedious.

One of the notions implicit in most evolutionary models is that the tree of life has a common root. In other words all individuals of all species represent end points of lineages which ultimately coalesce back to the the original common ancestor. The first Earthling, so to speak. I say implicit because common ancestry isn’t necessary for evolution to be valid; after all, we presumably accept that evolutionary process is operative in an exobiological context, if such a context exists. Therefore it is possible that modern extant lineages are derived from separate independent antecedents. A “multiple garden” model. This has seemed less and less plausible as the molecular basis of biology has been elucidated; it looks like the basic toolkit is found all across the tree of life. But with a new found awareness of the power of processes such as horizontal gene transfer the open & shut case is faced with a new element of ambiguity. Or perhaps not?

The idea that life forms share a common ancestor is “a central pillar of evolutionary theory,” says Douglas Theobald, a biochemist at Brandeis University in Waltham, Massachusetts. “But recently there has been some mumbling, especially from microbiologists, that it may not be so cut-and-dried.”

Because microorganisms of different species often swap genes, some scientists have proposed that multiple primordial life forms could have tossed their genetic material into life’s mix, creating a web, rather than a tree of life.

To determine which hypothesis is more likely correct, Theobald put various evolutionary ancestry models through rigorous statistical tests. The results, published in the May 13 Nature, come down overwhelmingly on the side of a single ancestor.

A universal common ancestor is at least 102,860 times more probable than having multiple ancestors, Theobald calculates.

The paper is now on the Nature website, A formal test of the theory of universal common ancestry. They looked specifically at 23 very conserved proteins across 12 taxa from the three domains of life (those being eukaryotes, prokaryotes, and the archaea). Here’s where the author explains the philosophy behind the statistical technique: Read More

Ancient DNA set to rewrite human history. Good overview by Rex Dalton at Nature. I assume he knows more than he’s letting on, so a bit of Kremlinology: “In March, the group reported the mitochondrial DNA sequence from this individual, an unknown hominin that, so far, does not genetically match either Neanderthals or H. sapiens and may represent a new species. The team dated the bone to about 40,000 years ago, but others say that the sediments around the bone may be as old as 100,000 years. There is speculation that the bone could be the remains of an older species of Homo, perhaps even of a remnant population of Homo heidelbergensis, known in Europe from 300,000 to 500,000 years ago, or of Homo erectus, found as early as 1.8 million years ago from Africa to Indonesia. A full sequence may help to resolve this.” I think we’ll know a lot more about X-woman and how she relates to us in the near future.

Neanderthals’r’us? A paleoanthropologist’s view. He claims that the genetics is finally aligning with the fossils.

The Neandertal fraction. John Hawks explains what it means to say that 1-4% of non-African ancestry is Neandertal when we always talk about how we’re 98-99% identical to chimpanzees. This came up in the comments but I didn’t address it because a little thought makes this pretty obvious, but now you can read John Hawks’ explanation if you need a boost.

Below is a video of the assault on a Swedish artist who drew Muhammad as a dog. He was at a university event celebrating free speech. People are shouting“Allahu Akbar!” Charming.Read More

Carl Zimmer asks “Will Anyone In Alabama Speak For Evolution?” The story is that a Republican candidate for governor in Alabama is being accused of not being a Creationist, and he is asserting that he is a Creationist. Some people might be surprised by this, but this is Alabama. It is famously well known that the general public tends to split down the middle in regards to evolution, and that there is a class aspect to the division. But what’s the breakdown by region? The GSS can help.

Let’s look at two variables:

SCITEST4: In your opinion, how true is this? Human beings developed from earlier species of
animals

Economists in the last few years have been shifting toward testing their theoretical models, whether through the experiments of behavioral economics, or, “natural experiments.” The reason economists have had issues with testing their models is that experimentation on humans has some natural constraints. Macroeconomists have an even greater problem, as experimentation on whole societies not only presents ethical conundrums, but there’s no way to fund or implement experiments on this scale. Macroeconomists turn out to be the paleontologists of economics.

Of course economists aren’t the only ones who’ve had this sort of problem with humans. The reason that geneticists focused on organisms such as flies, mice and fish is partly that these taxa breed fast and are easy to maintain in laboratories. But obviously there are things you can do, such as mutagenesis, with model organisms which you can not do with humans. Human genetics has traditionally relied on “natural experiments” of a sort, inbred lineages, recurrent recessive diseases, etc. Genetics has been a supplementary handmaid to medicine by and large. But sometimes history can load the die in genetics’ favor as well.

During the “Columbian Exchange” the New and Old World engaged in a massive transfer of ideas and individuals. The Old World received potatoes, maize, and tomatoes (to name a few). The New World…well, the New World received black people and white people. As documented in works such as 1491 the indigenous populations of the New World collapsed with the introduction of Old World diseases. Native peoples disappeared from the Caribbean, and were marginalized on the mainland excepting ecologically remote (e.g., the Guatemalan highlands) or forbidding (e.g., the Peruvian highlands) regions. But of course despite the obliteration of indigenous cultural self-consciousness and identity, the native populations did not totally disappear, they persisted genetically in the numerically dominant mestizo populations of much of Latin America. You don’t need genetics to understand what happened, books like Mestizaje in Ibero-America outline in detail using conventional historical archives how Spanish men arrived in New World and entered into relationships with indigenous women. Often several at a time, in contravention of the Catholic Church’s requirement of monogamy.

But in the post-genomic era we have more to go on than impressions, we can quantitize the extent and nature of the admixture, something of importance when considering medical research. A new paper in PNAS adds some more to the growing body of results on Latin American genomics by including populations which have traditionally been overlooked, and also putting a spotlight on the long term impact of sex-biased admixture. Genome-wide patterns of population structure and admixture among Hispanic/Latino populations:Read More

Templeton disproves gene analysis that appeared to support out-of-Africa replacement model. This is from a Washington U. press release, but the title is still obnoxious. The term “prove” and “disprove” should be used sparingly in science (though perhaps there are others out there who disagree, I’d like some reasons laid out for why they shouldn’t be used only in exceptional circumstances). Remember that I pointed to a controversy between Alan Templeton and computational biologists who used a Bayesian phylogenetic framework a few weeks ago. Templeton is claiming that the Neandertal admixture findings vindicate him. Certainly one does need to revisit models which assume that admixture may have occurred, but only below a threshold of 1%, when the current research indicates 1% to be the low bound. But I don’t think we need to fall into the trap of separating the world into the light and the dark; people may be right for the wrong reasons, and methods may be wrong because of faulty axioms. And who knows, Paabo & company may be in error. It happens.

The Psychological Diversity of Mankind. Like the rational actor model of economics there is some utility in focusing on the interindividual invariant aspects of cognition. But at some point you’ve squeezed all the juice out, and need to move on. Those of us who tend toward the neuroatypical side have intuitively understood that humans exhibit psychological diversity, because we’ve been looking in from outside the circus tent, whether we know it or not.

(2) The study of the upper limit of body size must address extrinsic as well as intrinsic factors, and it must be determined whether this limit is set by the bauplan of the organisms or by physical and ecological constraints imposed by the environment. Among several possible approaches, we chose the resource perspective because it has been shown that resource availability and maximal body size correlate closely (Burness et al., 2001).

(3) In the interplay of the biology of sauropod dinosaurs with their environment, a unique combination of plesiomorphic features (i.e., inherited from their ancestors) and evolutionary novelties emerge as the key for a more efficient use of resources by sauropods than by other terrestrial herbivore lineages. Plesiomorphic features of sauropods were many small offspring, the lack of mastication and the lack of a gastric mill. The evolutionary innovations were an avian-style respiratory system and a high basal metabolic rate.

(4) We posit that the long neck of sauropods was central to the energy-efficient food uptake of sauropods because it permitted food uptake over a large volume with a stationary body.

(5) In the Late Triassic and Early Jurassic (210–175 million years ago), the combination of biological properties listed above led to an evolutionary cascade in the sauropodomorph lineage characterized by selection for ever larger body size, mainly driven by predation pressure from theropod dinosaurs.

(6)From the Middle Jurassic onward, sauropod dinosaurs dominated global terrestrial ecosystems only to succumb to the catastrophic environmental change at the end of the Cretaceous 65 million years ago.

And here’s a schematic illustrating the interplay of evolutionary forces & constraints:Read More

One of the most successful achievements of the “post-genomic era” has been the elucidation of the genetic architecture which undergird the variation in human pigmentation. I like to point out that in 2005 the geneticist Armand Leroi observed in his book Mutants that we didn’t know the genetics of normal variation in relation to the trait of skin color. In 2010 one couldn’t plausibly write that. We know the genes which control the vast majority of the interpopulational variation in human complexion. This is not due to human ingenuity, but the fortuitous hand that nature dealt us. Pigmentation is a very salient phenotype, evident by the classification of genetically very distinct populations in Africa, India and Oceania as “black.” But in terms of a genetic research project it has long been one of the ways to explore patterns of inheritance in model organisms such as mice, in particular in relation to coat patterns and pigment. And luckily for us, many of the genes which are implicated in pigment variation produce similar changes across diversetaxa. Additionally, the genetic architecture of human pigmentation variation is such that most of the variance is concentrated among a few loci of large effect. Concretely, it seems that well over 50% of the African-European difference in skin color as measured by reflectance of visible light is attributable to two genes, SLC24A5 and KITLG. In Europeans around 75% of the dichotomous variation between those with blue and non-blue eyes may be due to changes in the genomic region across HERC2 and OCA2 (these two genes are very near each other). These are the veritable low hanging fruit, amenable to studies with even small sample sizes and modest statistical power, so strong are the effects of the genetic variables.

And why is pigment important? Obviously there are social ramifications. But pigmentation is likely a major target of natural selection as well, as I suggested in relation to Neandertals. The results are sometimes confusing, but it does seem that pigmentation related loci are enriched in relation to those genomic regions which turn up as positive in tests of natural selection. Additionally, looking at variation around those genes which are correlated with lighter skin across Eurasia it also seems that it may be that our own lineage has become somewhat paler within the last 20,000 years, perhaps even more recently. And the same may have been true for our possible Neander-kin.

At the current rate in regards to pigmentation the age of revolutionary science may soon be over. Extraction of ancient DNA will probably resolve the rate and nature of evolutionary change, while further typing of current populations will flesh out our understanding of the variants responsible for normal human variation. To do that requires more than simply larger sample sizes or improved genomic techniques, it also requires better measurement. The utilization of reflectance indices in studies of study skin color are a step in the right direction, but a new paper in PLoS Genetics points the way toward the same in the study of eye color, Digital Quantification of Human Eye Color Highlights Genetic Association of Three New Loci:Read More

If you haven’t checked out the “How It Should Have Ended” website, I really recommend it. I’m not a big consumer of web video excepting South Park and The Onion, but this is really good stuff. In particular this alternative ending of the originalIron Man is pretty amusing.

College Inc., a documentary about the for-profit diploma mills. As I’ve noted before, these institutions of higher education seem geared toward capturing federal dollars through grants and student loans by duping the less intelligent segments of the population into thinking that they can get a college degree. Many conservatives assume that the market can work miracles and produce firms which can educate the uneducable. Demand must be met by supply. Many liberals believe that everyone should have a college education and that everyone has the capability. The real problem is in secondary school.

Peter Heather’s new book, Empires and Barbarians: The Fall of Rome and the Birth of Europe, exhibits none of the minor faults which I noted in Diarmaid MacCulloch’s Christianity: The First Three Thousand Years. Heather manages to robustly balance the need for both breadth and depth, and I would even offer that this semi-sequel to his previous book, The Fall of the Roman Empire, is a superior piece of scholarship in relation to its predecessor (if a bit less compelling as narrative because of the weighting toward archaeology as opposed to literary sources). The author reports that he’s been working for 15 years on Empires and Barbarians, and it shows in the wide spread of sources and multidisciplinary nature of the argument. And that argument is in short an overturning the post-World War II orthodoxy among archaeologists, and a lesser extent historians, that cultural evolution occurs overwhelmingly through a process of the diffusion of memes, and is rarely accompanied by the flow or replacement of genes. This model is a counterpoint to the pre-World War II conception of the shift of language being a consequence of the shift of nations; ergo, it was once presumed that the rise of the English and the fall of the Celtic British occurred via the driving out of the latter by the former toward the maritime fringes of Wales and Cornwall. After World War II the sources were reinterpreted so that the Anglo-Saxon tribes were refashioned into very small compact bands of warriors who toppled the old Roman-British elite, and imposed their own language and cultural forms on the local populace (Norman Davies’ takes this model as the default in The Isles). If this was the outlook when it came to Britain, which became England and witnessed the extinction of the Celtic and Latin languages as well as the Christian religion with the arrival of the Germans, then naturally an even more skeptical take on mass migration would hold for the post-Roman German states of the Franks, Visigoths and Lombards who had a far more marginal cultural affect on the local Roman population (in late antiquity and the early Dark Ages the sources distinguish between the indigenous Romans and the various Germanic tribes decades after the fall of the Western Empire). In Empires and Barbarians Peter Heather reiterates that the view that the German tribes replacing the Roman era populations is false. But, he also objects strongly to the post-World War II consensus which would tend to minimize the extent of migration, population movement, and demographic displacement. In short, Heather wishes to rehabilitate the Völkerwanderung.Read More

Digital Quantification of Human Eye Color Highlights Genetic Association of Three New Loci. I was going to blog this, but obviously I got distracted. The best part of this paper is that they used a quantitative measure of eye color differences, instead of categorical binning. They confirmed the importance of the HERC2-OCA2 region in blue vs. brown eye color differences, but by using a more fine-grained description of the phenotype managed to smoke out other loci.

Is Mental Illness Good For You? One issue which I am much more conscious of now than I was a few years ago are the cultural preconditions for mental illness diagnosis. I come from a background predisposed to accept the maxim “chemistry for better living,” so I have no deep fear of drugs. But, I know people in my own life who have been put on anti-depressant medication almost as a preventative measure, and, last year I read The Vertigo Years: Europe 1900-1914. The book is not about mental illness, but I was struck by how many obviously culturally constructed mental illnesses existed which we don’t even remember now. This is not to deny real mental illness which is a function of biological abnormalities, or environmental stress or shock. But the very high penetration of diagnoses of mental illness should be viewed with skepticism, and needs no deep evolutionary explanation. It’s culture.

I assume by now that everyone has read A Draft Sequence of the Neandertal Genome. It’s free to all, so you should. At least look at the figures. Also, if you haven’t at least skimmed the supplement, you should do that as well. It’s nearly 200 pages, and basically feels more like a collection of minimally edited papers than anything else. There’s no point in me reviewing the paper, since you can read it, and plenty of others have hit the relevant ground already.

Since there seem to be three main segments of the paper, here are a few minimal thoughts on each.Read More

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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!